CRAN Package Check Results for Package polyRAD

Last updated on 2020-08-07 01:49:55 CEST.

Check Details

Version: 1.2
Check: installed package size
Result: NOTE
     installed size is 8.3Mb
     sub-directories of 1Mb or more:
     extdata 3.7Mb
     libs 3.4Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.2
Check: Rd cross-references
Result: NOTE
    Undeclared package ‘BSgenome’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘isolocus_sorting.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘isolocus_sorting.Rmd’
    
    --- re-building ‘polyRADtutorial.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Allele frequencies for mapping population not found. Estimating.
    Genotype likelihoods not found. Estimating.
    Generating sampling permutations for allele depth.
    
    For example usage please run: vignette('qqman')
    
    Citation appreciated but not required:
    Turner, S.D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. biorXiv DOI: 10.1101/005165 (2014).
    
    Loading required package: BiocGenerics
    Loading required package: parallel
    
    Attaching package: 'BiocGenerics'
    
    The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
    The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
    The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
    Loading required package: GenomeInfoDb
    Loading required package: S4Vectors
    Loading required package: stats4
    
    Attaching package: 'S4Vectors'
    
    The following object is masked from 'package:base':
    
     expand.grid
    
    Loading required package: IRanges
    Error: package or namespace load failed for 'GenomeInfoDb' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
     there is no package called 'GenomeInfoDbData'
    Quitting from lines 437-440 (polyRADtutorial.Rmd)
    Error: processing vignette 'polyRADtutorial.Rmd' failed with diagnostics:
    package 'GenomeInfoDb' could not be loaded
    --- failed re-building ‘polyRADtutorial.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘polyRADtutorial.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-macos-x86_64